Over the last few months we've noticed that several files were mysterously adding newlines to the end of php files after the ?>
Now this is bad because that new line is now HTML and it can cause all sorts of troubles on some servers.
We finally tracked it back to me. It turns out that everytime I saved it would put a newline at the end of the file if there was one there. Now comes the really fucked up part, inside the program itself I couldn't see it. It would show/act like there was no newline.
So I had to kill it. Lets hope edit plus 2 is better.